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All,

We're setting up a new cluster (based on CentOS 8) but have many users that still want to run older versions of FreeSurfer (5.3 and 5.3-HCP).
We're hitting a perl error which appears to be a known issue with newer versions of Perl:

[mtobias@login02 mri]$ mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
/mnt/beegfs/scratch/mtobias/mri
/export/freesurfer/freesurfer-5.3.0-HCP/bin/mri_nu_correct.mni
--n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
nIters 1
$Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $
...
Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at /export/freesurfer/freesurfer-5.3.0-HCP/mni/bin/nu_estimate_np_and_em line 165.
nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280)
ERROR: nu_correct

One fix suggested for Ubuntu users is to install an older version of Perl.  While we've tried that on our system, it seems the perl scripts are hard-wired to use /usr/bin/perl:

[root@mgt bin]# head -1 nu_estimate_np_and_em
#!/usr/bin/perl -w

So without replacing the system perl on every system in the cluster, is anyone aware of any other work-arounds for this issue?

Cheers,
Malcolm

 

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